[ENH] BEP022 - Magnetic Resonance Spectroscopy #425
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markmikkelsen
changed the title
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@markmikkelsen one of them has an excellent README but the 2 others have none There is a README template in the bids starter kit if that can help: https://github.com/bids-standard/bids-starter-kit/blob/main/templates/README.MD?plain=1 |
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@effigies do you think we should / could use this PR to use citation.cff files? I think we do not have any example that make use of them. |
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Not unless Mark already has CITATION.cff files he wants to include. We don't need to pile on tasks to this BEP. Let's make a separate PR that adds a citation file to an existing example. |
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oh yeah of course!! that's fair! will open an issue to see if we can actually do it in another dataset that already exist. |
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Yep! I've just added these files. |
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This pull request is nearly ready for merging. The check failures relate to the MRS filename suffices not being included in the |
- Change suffix from `ref` to `mrsref` where applicable
- Amend dataset_listing.tsv and README.md
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I'm continually having issues with the creation of this file. Not sure what I'm doing wrong when trying to add the MRS datasets (through print_dataset_listing.py).
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should be fixed
some things will have to be updated the BEP is merged and pybids has been updated
| @@ -2,7 +2,7 @@ name description link to full data maintained by datatypes suffixes | |||
| eeg_matchingpennies Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) [link](https://doi.org/10.17605/OSF.IO/CJ2DR) [@sappelhoff](https://github.com/sappelhoff) eeg channels, eeg, events | |||
| eeg_rishikesh Mind wandering experiment. EEG data in Biosemi (.bdf) format [link](https://openneuro.org/datasets/ds001787) [@arnodelorme](https://github.com/arnodelorme) eeg channels, eeg, events | |||
| eeg_face13 Deconstructing the early visual electrocortical response to face and house stimuli. EDF format [@andesha](https://github.com/andesha) eeg channels, coordsystem, eeg, electrodes, events | |||
| eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) eeg, beh channels, eeg, events, participants, scans | |||
| eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans | |||
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those changes were made by the script print_dataset_listing.py
| @@ -57,7 +57,7 @@ pet003 T1w, PET, blood [@mnoergaard](https://github.com/mnoergaard) anat, pet T | |||
| pet004 PET, blood [@mnoergaard](https://github.com/mnoergaard) pet blood, pet | |||
| pet005 T1w, PET [@mnoergaard](https://github.com/mnoergaard) anat, pet T1w, events, pet | |||
| micr_SEM Example SEM dataset in PNG format with 1 sample imaged over 2 sessions [link](https://doi.org/10.5281/zenodo.5498378) [@jcohenadad](https://github.com/jcohenadad) micr SEM, photo, samples, sessions | |||
| micr_SEMzarr Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions [@TheChymera](https://github.com/TheChymera) micr SEM, samples, sessions | |||
| micr_SEMzarr Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions [@TheChymera](https://github.com/TheChymera) micr SEM, SPIM, samples, sessions | |||
| @@ -72,6 +72,9 @@ ieeg_epilepsy multiple sessions, tutorial [link](https://neuroimage.usc.edu/bst/ | |||
| ieeg_epilepsyNWB multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative [link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids) [@TheChymera](https://github.com/TheChymera) anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, scans | |||
| ieeg_epilepsy_ecog multiple sessions, tutorial [link](https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog) [@ftadel](https://github.com/ftadel) anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans | |||
| ieeg_visual_multimodal [@irisgroen](https://github.com/irisgroen) anat, fmap, func, ieeg T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | |||
| genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, fmap, func FLAIR, T1w, bold, dwi, events, info, magnitude1, phasediff | |||
| genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, func FLAIR, T1w, bold, dwi, events, info | |||
| motion_dualtask older and younger participants walking while performing discrimination task [@sjeung](https://github.com/sjeung) eeg, motion channels, eeg, events, motion, scans | ||
| motion_spotrotation participants rotated heading using full-body motion or joystick [link](https://openneuro.org/datasets/ds004460) [@sjeung](https://github.com/sjeung) eeg, motion channels, coordsystem, eeg, electrodes, events, motion, scans | ||
| mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat T1w |
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the mrs datatypes and associated suffixes do not appear yet because those columns are updated by relying on pybids that does not know yet about those new things.
I would suggest finishing updating the table and README once the BEP is merged and we have updated pybids accordingly
README.md
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changes made automatically to the README with the print_dataset_listing.py script
This pull request adds MRS BIDS-compliant datasets to the
bids-examplesrepository. It includes three datasets:mrs_2dmrsi/,mrs_biggaba/, andmrs_fmrs/.